This invention relates to new oligonucleotide analogs. In particular, it relates to oligonucleotide analogs that have new substitute linkages in place of one or more of the phosphodiester linkages found in native DNA or RNA. Methods to synthesize the oligomers are described along with methods to use the oligomers as diagnostic reagents, or probes.
The use of oligomers (oligonucleotides and oligonucleotide analogs) as diagnostic reagents and probes is based on their ability to form duplex or triplex structures with complementary base sequences in target nucleic acids. Oligomers have also been used to inhibit gene expression by sequence-specific binding to target RNA sequences, "antisense inhibition", in living cells (for example see: Wagner et al, Science (1993) 260:1510-1513; Woolf et al, Nucleic Acid Res (1990) 18:1763-1769). In these studies, oligomers were introduced into cells using means such as microinjection or transfection to enhance the intracellular oligomer concentration. Antisense inhibition of gene expression using oligomers has been extensively described (Milligan et al, I Med Chem (1993) 36:1923-1937; Uhlmann et al, Chem Reviews (1990) 90:543-584; and Stein et al, Cancer Res (1988) 48:2659-2668). Another approach, referred to herein as "triple helix" therapy utilizes oligomers that bind to duplex DNA in a sequence-specific manner via "Hoogsteen" base pairing (Beal et al, Science (1991) 251:1360-1363; Young et al, Proc Natl Acad Sci (1991) 88:10023-10026). Both antisense and triple helix therapies exert therapeutic effects via binding to nucleic acid sequences that are responsible for establishing or maintaining disease conditions. Such sequences are found in the genome of pathogenic organisms including bacteria, protozoa, yeasts, parasites, fungi or viruses or may be endogenous sequences (oncogenes). By modulating the expression of a gene important for establishment, maintenance or elimination of a disease condition, the corresponding condition may be cured, prevented or ameliorated.
Another therapeutic approach that is based on the use of oligomers includes generation of "aptamers", oligomers that bind to intracellular or extracellular target molecules such as polypeptides or enzymes thereby interfering with their function (Bock, et al, Nature (1992) 355:564-566; PCT/US92/01383). Aptamers have successfully blocked target protein function in vivo (Griffin, et al, Blood (1993) 81:3271-3276). The use of oligomers for other therapeutic applications has been described (PCT/US91/01822). The invention oligomers can thus be used in applications where base pairing competence is not needed.
An important feature of oligomers is the type of backbone or linkage between adjacent nucleomonomers (nucleotides, nucleosides or their analogs) in an oligomer. Specifically, the backbone should contain internucleoside linkages that are stable in vivo and should be structured such that the oligomer is resistant to endogenous nucleases. At the same time, the oligomer must also retain its ability to hybridize to the target DNA or RNA.
A need exists for oligomers that are easy to synthesize, that are nuclease resistant, or have other useful properties such as improved permeation into cells.
It is an object of this invention to provide oligomers with substitute linkages that are easy to synthesize and that retain their ability to hybridize to complementary nucleic acid sequences.
These and other objects of the invention will be apparent from consideration of the specification as a whole.